scholarly journals Deviation from Hardy–Weinberg equilibrium, and temporal instability in allele frequencies at microsatellite loci in a local population of Atlantic cod

2005 ◽  
Vol 62 (8) ◽  
pp. 1588-1596 ◽  
Author(s):  
Sten Karlsson ◽  
Jarle Mork
Keyword(s):  
Microsatellite Loci ◽  
Atlantic Cod ◽  
Local Population ◽  
Allele Frequencies ◽  
Null Alleles ◽  
P Value ◽  
Patchy Distribution ◽  
Hardy Weinberg Equilibrium ◽  
The One ◽  
Weinberg Expectation

Abstract A total of 1455 spawning cod, sampled from a local spawning area in Trondheimsfjord (Norway) between 1985 and 2002, was screened at the microsatellite loci Gmo132 and Gmo2. Samples from 15 spawning years comprising 29 consecutive cohorts were analysed. At the Gmo132 locus, but not at Gmo2, allele frequencies varied significantly among sampling years as well as cohorts, corresponding to FST-values of 0.004 and 0.006, respectively. Both loci showed examples of significant deviations from Hardy–Weinberg expectation within sampling years as well as cohorts, manifested as deficiencies of heterozygotes. Combining the p-values from the single tests (Fisher's method) revealed an overall significant p-value for deviation from the Hardy–Weinberg expectations at Gmo132 but not at Gmo2. Trend tests showed significant HW deficiencies at both loci for annual samples but not for cohorts. Possible reasons for the deficiencies were discussed; inter alia the existence of null alleles, or a form of pseudo Wahlund effect due to a patchy distribution of habitats for settling O-group cod in the Trondheimsfjord. It was noted that there might be a relationship between the relatively high temporal within-population variability of allele frequencies at Gmo132 and the fact that among microsatellite loci studied so far, Gmo132 is the one that usually shows the highest genetic differentiation geographically in cod.

scholarly journals Validation and characterization of thirteen microsatellite markers for queen conch, Lobatus gigas

2016 ◽  
Author(s):  
Nathan K Truelove ◽  
Loong Fai Ho ◽  
Richard F Preziosi ◽  
Stephen J. Box
Keyword(s):  
Microsatellite Markers ◽  
Microsatellite Loci ◽  
Null Allele ◽  
Florida Keys ◽  
Illumina Miseq ◽  
Allele Frequencies ◽  
Null Alleles ◽  
Queen Conch ◽  
Hardy Weinberg Equilibrium

We report the development and characterization of 13 novel microsatellite loci for the Caribbean queen conch, Lobatus gigas, an ecologically and commercially important marine gastropod. Paired-end sequencing was carried out on genomic DNA from a single queen conch using half a flow cell lane of an Illumina MiSeq. A total of 48 potentially amplifiable loci containing microsatellites were tested on 45 individuals from the Florida Keys and Bahamas. In total, 13 consistently amplifying and polymorphic microsatellite loci were identified. The number of alleles ranged from 4 to 26 and observed heterozygosities ranged from 0.340 to 1.00. There was no evidence of scoring error, large allele dropout, or evidence of linkage disequilibrium at any locus. Four loci deviated from Hardy-Weinberg equilibrium due to moderate levels of null alleles (null allele frequencies ranged from 0.081 to 0.230). Although null alleles were detected at four microsatellite loci, the high levels of polymorphism and moderate null allele frequencies suggest that these 13 novel microsatellite markers will be useful for researchers carrying out conservation genetic studies of L. gigas.

scholarly journals Validation and characterization of thirteen microsatellite markers for queen conch, Lobatus gigas

2016 ◽  
Author(s):  
Nathan K Truelove ◽  
Loong Fai Ho ◽  
Richard F Preziosi ◽  
Stephen J. Box
Keyword(s):  
Microsatellite Markers ◽  
Microsatellite Loci ◽  
Null Allele ◽  
Florida Keys ◽  
Illumina Miseq ◽  
Allele Frequencies ◽  
Null Alleles ◽  
Queen Conch ◽  
Hardy Weinberg Equilibrium

We report the development and characterization of 13 novel microsatellite loci for the Caribbean queen conch, Lobatus gigas, an ecologically and commercially important marine gastropod. Paired-end sequencing was carried out on genomic DNA from a single queen conch using half a flow cell lane of an Illumina MiSeq. A total of 48 potentially amplifiable loci containing microsatellites were tested on 45 individuals from the Florida Keys and Bahamas. In total, 13 consistently amplifying and polymorphic microsatellite loci were identified. The number of alleles ranged from 4 to 26 and observed heterozygosities ranged from 0.340 to 1.00. There was no evidence of scoring error, large allele dropout, or evidence of linkage disequilibrium at any locus. Four loci deviated from Hardy-Weinberg equilibrium due to moderate levels of null alleles (null allele frequencies ranged from 0.081 to 0.230). Although null alleles were detected at four microsatellite loci, the high levels of polymorphism and moderate null allele frequencies suggest that these 13 novel microsatellite markers will be useful for researchers carrying out conservation genetic studies of L. gigas.

Characterization of 17 novel microsatellite loci in the Nile monitor (Varanus niloticus) via 454 pyrosequencing

2016 ◽  
Vol 37 (1) ◽  
pp. 121-125 ◽  
Author(s):  
Jared P. Wood ◽  
Todd S. Campbell ◽  
Robert B. Page
Keyword(s):  
Microsatellite Loci ◽  
454 Pyrosequencing ◽  
Sequence Similarity ◽  
Null Alleles ◽  
The Us ◽  
Hardy Weinberg Equilibrium ◽  
The City ◽  
Two Populations ◽  
Genotypic Disequilibrium

We used 454 pyrosequencing to characterize 17 novel microsatellite loci from the Nile monitor (Varanus niloticus), using samples from an invasive population in the US state of Florida. These markers were screened for variation in 40 individuals from the City of Cape Coral. Observed heterozygosity ranged from 0.18 to 0.73 (mean ± SE = 0.46 ± 0.06) and the number of alleles per locus ranged from 1 to 4 (mean ± SE = 2.5 ± 0.2). Preliminary genotyping of samples from populations in West Palm Beach and Homestead revealed two loci (Mon6andMon15) that are monomorphic in Cape Coral, but polymorphic in these other two populations. We found no statistical departures from Hardy-Weinberg equilibrium or evidence of null alleles. However, there was statistical evidence for genotypic disequilibrium betweenMon1-Mon14andMon3-Mon8. BLASTn searches of NCBI’s nr/nt database identified four microsatellites containing 454 fragments that exhibit substantial sequence similarity to loci in other reptilian genomes, suggesting these markers should be prioritized by researchers interested in cross-amplification in other varanids. The resources we have developed will enable investigations of the population genetic dynamics of invasive Nile monitors in Florida and may facilitate studies within this species native range.

Genetic variation within and relationships among five subpopulations of Slovak Thoroughbred

2004 ◽  
Vol 52 (3) ◽  
pp. 259-265
Author(s):  
Daniela Šátková-Jakabová ◽  
J. Trandžík ◽  
Ľudmila Hudecová-Kvasňáková ◽  
Erika Hegedüšová-Zetochová ◽  
A. Bugarský ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Genetic Variation ◽  
Genetic Differentiation ◽  
International Society ◽  
Microsatellite Loci ◽  
Genetic Relationships ◽  
Allele Frequencies ◽  
Weinberg Equilibrium ◽  
Hardy Weinberg Equilibrium

Genetic variation at six microsatellite loci was analysed for five Thoroughbred subpopulations to determine the magnitude of genetic differentiation and the genetic relationships among the subpopulations. Significant deviations from Hardy-Weinberg equilibrium were shown for a number of locus-population combinations, with all subpopulations. The genetic diversities and relationships of five Thoroughbred subpopulations were evaluated using six microsatellites recommended by the International Society of Animal Genetics (ISAG). The allele frequencies, the effective numbers of alleles, and the observed and expected heterozygosities were calculated. POPGENE v. 1.31 (Yeh et al., 1997) was used to test for deviations from the Hardy-Weinberg (H-W) equilibrium and to assign FIS estimates (Weir, 1990). The utility of microsatellites for evaluating genetic diversity of horses is discussed.

Development and characterization of new polymorphic microsatellite loci for Trionyx triunguis (Testudines: Trionychidae) in the Mediterranean Basin

2015 ◽  
Vol 36 (3) ◽  
pp. 318-324 ◽  
Author(s):  
Özgür Güçlü ◽  
Salih Hakan Durmuş ◽  
Kamil Candan ◽  
Nurettin Beşer ◽  
Süheyla Türkyilmaz ◽  
...  
Keyword(s):  
Microsatellite Loci ◽  
Captive Breeding ◽  
Null Alleles ◽  
Enriched Library ◽  
Hardy Weinberg Equilibrium ◽  
Polymorphic Microsatellite ◽  
The Mediterranean ◽  
Captive Breeding Programs

The Mediterranean subpopulation of T. triunguis has been listed by IUCN as critically endangered (European Reptile and Amphibian Specialist Group 1996, category CR C2A). There are very few studies for determination of distribution and population genetics of this species in the world. A total of 13 polymorphic microsatellite loci were isolated from 42 samples of T. triunguis by using biotinylated (GT)10, (CT)10, (GATA)5-enriched library. The range of observed heterozygosities was 0.000-0.833 with a mean of 0.274, and the range of expected heterozygosities was 0.081-0.607 with a mean of 0.374. It was found that four loci deviated significantly from Hardy-Weinberg equilibrium after Bonferroni correction analysis. There was no evidence for large allele dropout. Null alleles may be present at ttmed-6, ttmed-8, and ttmed-9 loci, as suggested by the general excess of homozygote for most allele size classes. Designed microsatellite loci could provide a powerful tool for the population structure and conservation genetics studies of the Nile soft-shelled turtle and for captive breeding programs or to detect species illegal trade.

New Microsatellite Markers for Two Sympatric Tinamou Species, the Ornate Tinamou (Nothoprocta ornata) and Darwin's Nothura (Nothura darwinii)

2016 ◽  
Vol 9 (3) ◽  
pp. 139-146 ◽  
Author(s):  
Lina Maria Giraldo Deck ◽  
Jan Christian Habel ◽  
Manuel Curto ◽  
Martin Husemann ◽  
Sarah Sturm ◽  
...  
Keyword(s):  
Microsatellite Loci ◽  
Life History Traits ◽  
Null Alleles ◽  
Genetic Population ◽  
Expected Heterozygosity ◽  
Hardy Weinberg Equilibrium ◽  
Polymorphic Microsatellite ◽  
Successful Amplification ◽  
Low Coverage ◽  
Candidate Loci

Tinamous (Tinamidae) represent one of the most ancient living avian lineages but their life history traits are relatively unstudied. Here we identified microsatellite loci for two sympatric tinamou species, the Ornate Tinamou ( Nothoprocta ornata) and the Darwin's Nothura ( Nothura darwinii) from low coverage Illumina sequencing of genomic DNA. The experiment yielded a large number of candidate loci. We designed primers and tested them for successful amplification in 1 to 2 populations of the target species, tested for deviation from the Hardy–Weinberg equilibrium and the presence of null alleles, the levels of polymorphism and potential cross-amplification. All 30 and 24 loci amplified consistently, in the Ornate Tinamou and in Darwin's Nothura, respectively. In the Ornate Tinamou, 25 loci were polymorphic and in the Darwin's Nothura 12, with 2 to 14 alleles per locus in both species. The expected heterozygosity ranged from 0.054 to 0.917 in the Ornate Tinamou and from 0.044 to 0.908 in the Darwin's Nothura. 23 (40%) of 54 loci were successfully cross-amplified. These newly discovered, polymorphic microsatellite loci represent a valuable tool for future studies on social behaviour, parentage and genetic population structure in tinamous.

scholarly journals Development and characterization of 26 novel microsatellite loci for the trochid gastropodGibbula divaricata(Linnaeus, 1758), using IlluminaMiSeqnext generation sequencing technology

PeerJ ◽  
2016 ◽  
Vol 4 ◽  
pp. e1789 ◽  
Author(s):  
Violeta López-Márquez ◽  
Ricardo García-Jiménez ◽  
José Templado ◽  
Annie Machordom
Keyword(s):  
Microsatellite Loci ◽  
High Throughput Sequencing ◽  
Illumina Miseq ◽  
Null Alleles ◽  
Sequencing Technology ◽  
Sympatric Distribution ◽  
Biogeographic Patterns ◽  
Hardy Weinberg Equilibrium ◽  
Significant Linkage

In the present study we used the high-throughput sequencing technology Illumina MiSeq to develop 26 polymorphic microsatellite loci for the marine snailGibbula divaricata. Four to 32 alleles were detected per locus across 30 samples analyzed. Observed and expected heterozygosities ranged from 0.130 to 0.933 and from 0.294 to 0.956, respectively. No significant linkage disequilibrium existed. Seven loci deviated from Hardy-Weinberg equilibrium that could not totally be explained by the presence of null alleles. Sympatric distribution with other species of the genusGibbula, asG. rarilineataandG. varia, lead us to test the cross utility of the developed markers in these two species, which could be useful to test common biogeographic patterns or potential hybridization phenomena, since morphological intermediate specimens were found.

Efektifitas Ekstrak Daun Sirih Hijau (Piper Betle) sebagai Insektisida Nabati terhadap Mortalitas Lalat Rumah (Musca domestica)

2019 ◽  
Vol 10 (2) ◽  
pp. 44-50
Author(s):  
Rinaldi Daswito ◽  
Rima Folentia ◽  
M Yusuf MF
Keyword(s):  
Musca Domestica ◽  
Leaf Extract ◽  
Effective Concentration ◽  
P Value ◽  
Piper Betle ◽  
Microbiology Laboratory ◽  
House Flies ◽  
Betel Leaf ◽  
The One ◽  
One Way Anova

One of the diseases that can be transmitted by flies is diarrhea. Green betel leaf contains essential oils, chavicol, arecoline, phenol, and tannins which function as plant-based insecticides. This study aimed to determine the effectiveness of green betel leaf extract (Piper betel) as a plant-based insecticide on the number of mortality of house flies (Musca domestica). The research was an experimental study used After Only Design used the One Way Anova test with a 95% confidence level. The samples used were 360 ​​house flies. Each treatment of 30 house flies with 4 repetitions and used three concentrations of green betel leaf extract (25%, 50%, 75%). The study was conducted at the Chemistry and Microbiology Laboratory of Health Polytechnic Tanjungpinang, while the location of the fly collection was at the Tokojo Garbage Collection Station in Bintan Regency. The number of mortality of house flies at a concentration of 25% was 81 heads (67.5%), 50% concentrations were 93 heads (77.5%), and at a concentration of 75% were 103 heads (85.83%). There was an effect of green betel leaf extract on the mortality of house flies (p-value 0.0001 <0.05) with the most effective concentration of 75%. Further research is needed to obtain a finished product utilizing green betel leaf extract as a vegetable insecticide, especially in controlling the fly vector. Need further research on the use of green betel leaf extract as a vegetable insecticide controlling the fly vector by taking into account the amount of spraying and the age of the fly.   Keywords: Green betel leaf extract , organic insecticide, houseflies

scholarly journals Comparison of Four Commercially Available Point-of-Care Tests to Detect Antibodies against Canine Parvovirus in Dogs

Viruses ◽  
2020 ◽  
Vol 13 (1) ◽  
pp. 18
Author(s):  
Michèle Bergmann ◽  
Mike Holzheu ◽  
Yury Zablotski ◽  
Stephanie Speck ◽  
Uwe Truyen ◽  
...  
Keyword(s):  
Test Performance ◽  
Point Of Care ◽  
Reference Method ◽  
Canine Parvovirus ◽  
P Value ◽  
Important Indicator ◽  
Specificity And Sensitivity ◽  
Specific Pathogen ◽  
The One ◽  
Point Of Care Tests

Measuring antibodies to evaluate dogs´ immunity against canine parvovirus (CPV) is useful to avoid unnecessary re-vaccinations. The study aimed to evaluate the quality and practicability of four point-of-care (POC) tests for detection of anti-CPV antibodies. The sera of 198 client-owned and 43 specific pathogen-free (SPF) dogs were included; virus neutralization was the reference method. Specificity, sensitivity, positive and negative predictive value (PPV and NPV), and overall accuracy (OA) were calculated. Specificity was considered to be the most important indicator for POC test performance. Differences between specificity and sensitivity of POC tests in the sera of all dogs were determined by McNemar, agreement by Cohen´s kappa. Prevalence of anti-CPV antibodies in all dogs was 80% (192/241); in the subgroup of client-owned dogs, it was 97% (192/198); and in the subgroup of SPF dogs, it was 0% (0/43). FASTest® and CanTiCheck® were easiest to perform. Specificity was highest in the CanTiCheck® (overall dogs, 98%; client-owned dogs, 83%; SPF dogs, 100%) and the TiterCHEK® (overall dogs, 96%; client-owned dogs, 67%; SPF dogs, 100%); no significant differences in specificity were observed between the ImmunoComb®, the TiterCHEK®, and the CanTiCheck®. Sensitivity was highest in the FASTest® (overall dogs, 95%; client-owned dogs, 95%) and the CanTiCheck® (overall dogs, 80%; client-owned dogs, 80%); sensitivity of the FASTest® was significantly higher compared to the one of the other three tests (McNemars p-value in each comparison: <0.001). CanTiCheck® would be the POC test of choice when considering specificity and practicability. However, differences in the number of false positive results between CanTiCheck®, TiterCHEK®, and ImmunoComb® were minimal.

Disequilibrium Coefficient: A Bayesian Perspective

2011 ◽  
Vol 10 (1) ◽  
Author(s):  
Helena Brentani ◽  
Eduardo Y Nakano ◽  
Camila B Martins ◽  
Rafael Izbicki ◽  
Carlos Alberto Pereira
Keyword(s):  
Bayesian Methods ◽  
Selection Pressure ◽  
Disease Susceptibility ◽  
Correlation Coefficients ◽  
Significance Test ◽  
Genotyping Error ◽  
Posterior Density ◽  
Hardy Weinberg Equilibrium ◽  
The One ◽  
Zero Equilibrium

Hardy-Weinberg Equilibrium (HWE) is an important genetic property that populations should have whenever they are not observing adverse situations as complete lack of panmixia, excess of mutations, excess of selection pressure, etc. HWE for decades has been evaluated; both frequentist and Bayesian methods are in use today. While historically the HWE formula was developed to examine the transmission of alleles in a population from one generation to the next, use of HWE concepts has expanded in human diseases studies to detect genotyping error and disease susceptibility (association); Ryckman and Williams (2008). Most analyses focus on trying to answer the question of whether a population is in HWE. They do not try to quantify how far from the equilibrium the population is. In this paper, we propose the use of a simple disequilibrium coefficient to a locus with two alleles. Based on the posterior density of this disequilibrium coefficient, we show how one can conduct a Bayesian analysis to verify how far from HWE a population is. There are other coefficients introduced in the literature and the advantage of the one introduced in this paper is the fact that, just like the standard correlation coefficients, its range is bounded and it is symmetric around zero (equilibrium) when comparing the positive and the negative values. To test the hypothesis of equilibrium, we use a simple Bayesian significance test, the Full Bayesian Significance Test (FBST); see Pereira, Stern and Wechsler (2008) for a complete review. The disequilibrium coefficient proposed provides an easy and efficient way to make the analyses, especially if one uses Bayesian statistics. A routine in R programs (R Development Core Team, 2009) that implements the calculations is provided for the readers.

Sign in / Sign up

Export Citation Format

Share Document